Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO2 fixation cycle in extremely thermoacidophilic archaea

Loder, Andrew J.; Han, Young-Tak; Hawkins, Aaron B.; Lian, Hong; Lipscomb, Gina L.; Schut, Gerrit J.; Keller, Matthew W.; Adams, Michael W. W.; Kelly, Robert M.

doi:10.1016/j.ymben.2016.10.009

Cited by 28 publications

(18 citation statements)

References 61 publications

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“…Cells are assumed to be 80% protein ( = 0.8), and the amount of this cell protein that is devoted to carbon fixation (ACC abundance, E fix ) is set at 2% in the faster-growing M. sedula and 1% in the slower-growing N. maritimus. The 2% value for M. sedula is known experimentally (Hügler et al, 2003;Loder et al, 2016), while the 1% N. maritimus value is consistent with proteomics data (Qin et al, 2018…”

Section: (2)supporting

confidence: 78%

CO2-dependent carbon isotope fractionation in Archaea, Part I: Modeling the 3HP/4HB pathway

Pearson

Hurley

Elling

et al. 2019

Geochimica et Cosmochimica Acta

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The 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) pathway of carbon fixation is found in thermophilic Crenarchaeota of the order Sulfolobales and in aerobic, ammonia-oxidizing Thaumarchaeota. Unlike all other known autotrophic carbon metabolisms, this pathway exclusively uses HCO 3rather than CO 2 as the substrate for carbon fixation. Biomass produced by the 3HB/4HP pathway is relatively 13 Cenriched compared to biomass fixed by other autotrophic pathways, with total biosynthetic isotope effects ( Ar) of ca. 3‰ in the Sulfolobales and ca. 20‰ in the Thaumarchaeota. Explanations for the difference between these values usually invoke the dual effects of thermophily and growth at low pH (low [ ]) HCO-3 for the former group vs. mesophily and growth at pH > 7 (high [ ]) for the latter group. Here we HCO-3 examine the model taxa Metallosphaera sedula and Nitrosopumilus maritimus using an isotope fluxbalance model to argue that the primary cause of different  Ar values more likely is the presence of carbonic anhydrase in M. sedula and its corresponding absence in N. maritimus. The results suggest that the pool of inside N. maritimus is out of isotopic equilibrium with CO 2 and that the organism imports < 10% HCO-3 from the extracellular environment. If correct and generalizable, the aerobic, ammonia-oxidizing HCO-3 marine Thaumarchaeota are dependent on passive CO 2 uptake and a slow rate of intracellular conversion to. Values of  Ar should therefore vary in response to growth rate () and CO 2 availability, analogous HCO-3 to eukaryotic algae, but in the opposite direction:  Ar becomes smaller as [CO 2(aq) ] increases and/or  decreases. Such an idea represents a testable hypothesis, both in the laboratory and in natural systems. Sensitivity to  and CO 2 implies that measurements of  Ar may hold promise as a pCO 2 paleobarometer. 3 CO 2-yet isotopically, it is distinct. The marked difference in  Ar values between thermoacidophilic Sulfolobales and the ammoniaoxidizing marine Thaumarchaeota is well recognized (e.g., Könneke et al., 2012; 2014) but has not yet been quantitatively explained. Explanation of the 20‰  Ar value in Thaumarchaeota generally invokes both

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Section: (2)supporting

confidence: 78%

CO2-dependent carbon isotope fractionation in Archaea, Part I: Modeling the 3HP/4HB pathway

Pearson

Hurley

Elling

et al. 2019

Geochimica et Cosmochimica Acta

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“…An array of proteins could be responsible for these activities: M. sedula genome harbors six crotonyl-CoA hydratase homologs ( Table 1 ), and four of them were previously characterized. One of these homologs was identified as 3-hydroxypropionyl-CoA dehydratase (Msed_2001) ( 15 , 18 ). This protein is universally conserved among autotrophic Sulfolobales ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

Convergent Evolution of a Promiscuous 3-Hydroxypropionyl-CoA Dehydratase/Crotonyl-CoA Hydratase in Crenarchaeota and Thaumarchaeota

Liu

Brown

Könneke

et al. 2021

mSphere

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The autotrophic 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle functions in thermoacidophilic, (micro)aerobic, hydrogen-oxidizing Crenarchaeota of the order Sulfolobales as well as in mesophilic, aerobic, ammonia-oxidizing Thaumarchaeota. Notably, the HP/HB cycle evolved independently in these two archaeal lineages, and crenarchaeal and thaumarchaeal versions differ regarding their enzyme properties and phylogeny. These differences result in altered energetic efficiencies between the variants. Compared to the crenarchaeal HP/HB cycle, the thaumarchaeal variant saves two ATP equivalents per turn, rendering it the most energy-efficient aerobic pathway for carbon fixation. Characteristically, the HP/HB cycle includes two enoyl coenzyme A (CoA) hydratase reactions: the 3-hydroxypropionyl-CoA dehydratase reaction and the crotonyl-CoA hydratase reaction. In this study, we show that both reactions are catalyzed in the aforementioned archaeal groups by a promiscuous 3-hydroxypropionyl-CoA dehydratase/crotonyl-CoA hydratase (Msed_2001 in crenarchaeon Metallosphaera sedula and Nmar_1308 in thaumarchaeon Nitrosopumilus maritimus). Although these two enzymes are homologous, they are closely related to bacterial enoyl-CoA hydratases and were retrieved independently from the same enzyme pool by the ancestors of Crenarchaeota and Thaumarchaeota, despite the existence of multiple alternatives. This striking similarity in the emergence of enzymes involved in inorganic carbon fixation from two independently evolved pathways highlights that convergent evolution of autotrophy could be much more widespread than anticipated. IMPORTANCE Inorganic carbon fixation is the most important biosynthetic process on Earth and the oldest type of metabolism. The autotrophic HP/HB cycle functions in Crenarchaeota of the order Sulfolobales and in ammonia-oxidizing Archaea of the phylum Thaumarchaeota that are highly abundant in marine, terrestrial, and geothermal environments. Bioinformatic prediction of the autotrophic potential of microorganisms or microbial communities requires identification of enzymes involved in autotrophy. However, many microorganisms possess several isoenzymes that may potentially catalyze the reactions of the cycle. Here, we studied the enzymes catalyzing 3-hydroxypropionyl-CoA dehydration and crotonyl-CoA hydration in Nitrosopumilus maritimus (Thaumarchaeota) as well as in Metallosphaera sedula (Crenarchaeota). We showed that both reactions were catalyzed by homologous promiscuous enzymes, which evolved independently from each other from their bacterial homologs. Furthermore, the HP/HB cycle is of applied value, and knowledge of its enzymes is necessary to transfer them to a heterologous host for synthesis of various value-added products.

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“…The HP/HB cycle is a perspective route for the conversion of CO 2 into liquid fuels and industrial chemicals and can be engineered for the production of value-added compounds like 3-hydroxypropionate or n-butanol (Hawkins et al, 2011(Hawkins et al, , 2013bKeller et al, 2013;Fuchs and Berg, 2014;Loder et al, 2016). The identification of highly specific thermophilic enzymes involved in this pathway expands opportunities for the application of the pathway.…”

Section: Discussionmentioning

confidence: 99%

“…in cell extract (Berg et al, 2007) Reaction (Nr. in Figure 1) Genes, according to Berg et al (2007) Genes, according to Loder et al (2016) Min. act.…”

Section: Methodsmentioning

confidence: 99%

Enzymes Catalyzing Crotonyl-CoA Conversion to Acetoacetyl-CoA During the Autotrophic CO2 Fixation in Metallosphaera sedula

2020

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Autotrophic Crenarchaeota use two different cycles for carbon dioxide fixation. Members of the Sulfolobales use the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle, whereas Desulfurococcales and Thermoproteales use the dicarboxylate/4hydroxybutyrate cycle. While these two cycles differ in the carboxylation reactions resulting in the conversion of acetyl-CoA + 2 CO 2 to succinyl-CoA, they have a common regeneration part in which succinyl-CoA is reconverted to two acetyl-CoA molecules. This common part includes crotonyl-CoA conversion to acetoacetyl-CoA, which has unequivocally been shown in Ignicoccus hospitalis (Desulfurococcales) and Pyrobaculum neutrophilus (Thermoproteales) to be catalyzed by a bifunctional crotonase/3-hydroxybutyryl-CoA dehydrogenase. It is a fusion protein consisting of an enoyl-CoA hydratase and a dehydrogenase domain. As the homologous bifunctional protein is present in Sulfolobales as well, its common functioning in the conversion of crotonyl-CoA to acetoacetyl-CoA was proposed. Here we show that a model autotrophic member of Sulfolobales, Metallosphaera sedula, possesses in addition to the bifunctional protein (Msed_0399) several separate genes coding for crotonyl-CoA hydratase and (S)-3-hydroxybutyryl-CoA dehydrogenase. Their genes were previously shown to be transcribed under autotrophic and mixotrophic conditions. The dehydrogenase Msed_1423 (and not the bifunctional protein Msed_0399) appears to be the main enzyme catalyzing the (S)-3-hydroxybutyryl-CoA dehydrogenase reaction. Homologs of this dehydrogenase are the only (S)-3-hydroxybutyryl-CoA dehydrogenases present in all autotrophic Sulfolobales, strengthening this conclusion. Two uncharacterized crotonase homologs present in M. sedula genome (Msed_0336 and Msed_0384) were heterologously produced and characterized. Both proteins were highly efficient crotonyl-CoA hydratases and may contribute (or be responsible) for the corresponding reaction in the HP/HB cycle in vivo.

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Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO2 fixation cycle in extremely thermoacidophilic archaea

Cited by 28 publications

References 61 publications

CO2-dependent carbon isotope fractionation in Archaea, Part I: Modeling the 3HP/4HB pathway

CO2-dependent carbon isotope fractionation in Archaea, Part I: Modeling the 3HP/4HB pathway

Convergent Evolution of a Promiscuous 3-Hydroxypropionyl-CoA Dehydratase/Crotonyl-CoA Hydratase in Crenarchaeota and Thaumarchaeota

Enzymes Catalyzing Crotonyl-CoA Conversion to Acetoacetyl-CoA During the Autotrophic CO2 Fixation in Metallosphaera sedula

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